Perhaps. It's likely a reflection of a cultural shift in the city and region.
With that said, I'm a big fan of local bars, pubs, and restaurants. Unironically. Cheap beer by the pint, bar pizza, roast beef sandwiches on a paper plate with Greek music tinkling out of the kitchen.
My fondest memory of the Barking Crab is holding a bathroom wastebasket for my then girlfriend (after an ill-considered shrimp cocktail). I think you and I are on the same page wanting to maintain reliable, casual, and affordable spots all over the city. I disagree that the three places kicked around in this thread are/were anything special.
I suspect that you hated these places because they were basically The Kells, Howl at the Moon, or any of the other soulless, empty, horrid places where the worst of all classes for some reason feel impelled to wait in long lines on Friday and Saturday nights. There's something so inherently Boston about these pseudo-"thing" places.. at least other cities have real club scenes, or actual swanky places (which I hate, but respect more than the bland try-hard-ness of these idiosyncratically Boston loser bars). Judgmental of me? You bet. I spent enough time exploring Boston's nightlife, or lack thereof, and the feeling of seeing the droves of people all overdressed and waiting outside to go to Whiskey Priest in December is a disgust I will not miss.
I do agree with Suffolk's comment, though, that on a sunny afternoon, these were very different places. The Atlantic Beer Garden was actually a decent outdoor relaxed place to go at a time like that... low key... which is becoming increasingly hard to find in this town.
Dives are great and yes, Beacon Hill's stranglehold on licenses, coupled with a city that kowtows to every neighborhood complaint, has allowed the death of nearly every dive bar in the city and of course, an impossibility to ever replacing them. Ayanna Presley be praised for fighting the good fight and getting more neighborhood licenses, but it's too late, for the most part... the legit spots are never coming back, because to be legit, in my opinion, you need to actually be a bar that keeps bar hours, and the neighborhoods, now gentrified, will fight any 1 or 2am closing time to the death. So all these new licenses are going to go to semi-upscale food-bars that close at midnight. So much for the good ol Boston dive. The few that are left are increasingly turning into a Disneyland version of what they once were... I mean, cmon, the line for the Sil has been around the corner now for over five years (?!) gimme a break.
Beton - what are your spots in Eastie? There's precious few left around my parts...
Although not my hood at all, Tavern at the End of the World is a fairly new spot that's one of the few to replicate what I think a decent normal bar should be like. Good place, but I haven't been in a couple years now. The Behan in JP, my favorite of them all, keeps it real... BK's in Rozzie, probably too real... The Corrib in Brookline used to be delightfully depressing, still around under a new name... The Last Drop in Brighton... There's a few others still left....